The R&B singer released a statement to CNN saying he and his group were asked to move on three separate occasions after security seated them in the church.
Brown says security then prevented him from seeing his and Houston's daughter Bobbi-Kristina.
He says in light of the events he gave a kiss to the casket of his ex-wife and departed so as to not create a scene.
Brown says his children are "completely distraught" over the incident.
He adds "this was a day to honor Whitney.
I doubt Whitney would have wanted this to occur.
I will continue to pay my respects to my ex-wife the best way I know how."
Brown reportedly left the New Hope Baptist Church in Newark, New Jersey just 20 minutes after the service began at noon.
The singer was already a subject of debate with regards to his attendance at Whitney's funeral.
Many have pointed the finger at Brown for Houston's personal problems over their tumultuous 15-year marriage that ended in 2007.
Earlier reports suggested that some members of Whitney's family did not want him at the service.
Houston died suddenly one week ago at the age of 48.
(Copyright 2012 by VERTEXNews/Newsroom Solutions)